Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_009546784.1 CCE_RS01385 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= BRENDA::A0A222AKA3 (368 letters) >NCBI__GCF_000017845.1:WP_009546784.1 Length = 343 Score = 154 bits (390), Expect = 3e-42 Identities = 106/326 (32%), Positives = 161/326 (49%), Gaps = 33/326 (10%) Query: 43 LLMYRAMVVGRAFNRQATAFSRQGRLAVYPSS-RGQEACQVGSALAVRPT-DWLFPTYRE 100 L++Y M +GR F + +GR+ + GQEA G A+RP D++ TYR+ Sbjct: 23 LMLYEDMTLGRLFEDKCAEMYYRGRMFGFVHLYNGQEAVSTGIIKALRPDEDYVSSTYRD 82 Query: 101 SVALLTRGIDPVQVLT-LFRGDQHC-------------------GYDPVTEHTAPQCTPL 140 V L+ G+ P +V+ LF + C GY V E P T Sbjct: 83 HVHALSCGVPPREVMAELFGKETGCSKGRGGSMHLFSEKHRLLGGYAFVAEGI-PVATGA 141 Query: 141 ATQCLHAAGLADAARMAGDPI---VALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQN 197 A Q + M GD V + + GDGA++ G F E LN AA+ + P++++V+N Sbjct: 142 AFQSKYRR------EMMGDETADQVTVCFFGDGASNNGQFFECLNMAALWKLPIIYVVEN 195 Query: 198 NQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLI 257 N++AI + + T+ + KA+ + M GV +DG DVL V + +A RARAG GPTLI Sbjct: 196 NKWAIGMAHNRATSQPEIYKKASVFDMVGVEVDGMDVLAVRKVAQEAIARARAGEGPTLI 255 Query: 258 EAVTYRIDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAAAD 317 EA+TYR H+ AD D R E W ++DP+ RLE L+ + +++ D I Sbjct: 256 EALTYRFRGHSLADPD-ELRSPDEKQFWGSKDPIQRLEAYLIEHNLANQSELDEIKQKVQ 314 Query: 318 AFAGELSARFSAPPTGDPMQMFRHVY 343 A + P DP +++R+V+ Sbjct: 315 ASVDDAVKFAEESPEPDPKELYRYVF 340 Lambda K H 0.319 0.132 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 231 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 368 Length of database: 343 Length adjustment: 29 Effective length of query: 339 Effective length of database: 314 Effective search space: 106446 Effective search space used: 106446 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory